Variant report

Variant	rs12125573
Chromosome Location	chr1:46734792-46734793
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:46734320-46734836	GM12892	blood:	n/a	n/a
2	POLR2A	chr1:46734423-46734989	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:46728001..46730178-chr1:46732904..46735671,2	K562	blood:
2	chr1:46712729..46715447-chr1:46734704..46736435,3	K562	blood:

Variant related genes	Relation type
RAD54L	TF binding region
ENSG00000085999	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10789488	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10890386	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10890387	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10890388	0.83[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11584233	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11586229	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12028248	0.87[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12039667	0.81[AMR][1000 genomes]
rs12044708	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12126187	1.00[MEX][hapmap]
rs12141269	1.00[MEX][hapmap]
rs12141928	0.93[MEX][hapmap]
rs1547180	0.92[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17102087	0.94[JPT][hapmap];0.86[MEX][hapmap]
rs2093044	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4660918	0.83[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4660919	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4660920	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4660921	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6429596	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6689182	0.96[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs6692775	0.87[CEU][hapmap];0.82[GIH][hapmap];0.83[EUR][1000 genomes]
rs6696085	1.00[MEX][hapmap]
rs7527133	0.86[AMR][1000 genomes]
rs953070	0.87[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9793263	0.88[ASW][hapmap];0.86[GIH][hapmap];0.93[LWK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv470711	chr1:46660295-46810530	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv829748	chr1:46724508-46876122	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12125573	NSUN4	cis	parietal	SCAN
rs12125573	MMACHC	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46713600-46743600	Weak transcription	Aorta	Aorta
2	chr1:46713800-46743400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:46714200-46743200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:46714200-46743400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:46714200-46743400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:46714200-46743600	Weak transcription	Gastric	stomach
7	chr1:46714200-46743800	Weak transcription	Right Atrium	heart
8	chr1:46714400-46736200	Weak transcription	Fetal Lung	lung
9	chr1:46714400-46743400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:46714400-46745400	Weak transcription	Fetal Brain Male	brain
11	chr1:46714400-46745600	Weak transcription	Fetal Kidney	kidney
12	chr1:46714400-46754200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:46714600-46736400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:46714600-46748600	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:46714600-46749600	Weak transcription	Fetal Heart	heart
16	chr1:46714800-46748400	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:46715000-46740800	Strong transcription	Fetal Stomach	stomach
18	chr1:46715000-46752800	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:46715200-46743400	Weak transcription	Spleen	Spleen
20	chr1:46715200-46748000	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr1:46715200-46748400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:46715200-46764200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:46715400-46748200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:46715400-46748400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:46715400-46748400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:46715400-46753000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:46715400-46754200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:46715400-46763800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:46715400-46764400	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:46715400-46765600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:46716000-46749400	Strong transcription	Fetal Thymus	thymus
32	chr1:46716200-46742800	Strong transcription	K562	blood
33	chr1:46717200-46748000	Strong transcription	Thymus	Thymus
34	chr1:46718200-46749600	Strong transcription	Dnd41	blood
35	chr1:46719800-46743200	Weak transcription	Brain Hippocampus Middle	brain
36	chr1:46720600-46750800	Strong transcription	Fetal Muscle Trunk	muscle
37	chr1:46720800-46766400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:46721400-46745000	Strong transcription	HepG2	liver
39	chr1:46721600-46753800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:46721800-46735200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:46721800-46743000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:46721800-46744200	Weak transcription	Primary T cells from cord blood	blood
43	chr1:46721800-46750600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:46723000-46743400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:46723200-46734800	Strong transcription	Duodenum Mucosa	Duodenum
46	chr1:46723200-46740800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:46723200-46743400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr1:46723200-46743400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr1:46723200-46743400	Weak transcription	Brain Substantia Nigra	brain
50	chr1:46723200-46747000	Strong transcription	H9 Cell Line	embryonic stem cell

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